I like them!
And aren't different colors of uniforms or shirts used on US aircraft carriers to quicky spot what part of the flightdeck crew someone belongs too?
Personally, I think it makes sence to have different colors, although I prefer the way the FC-style uniforms do it a bit more subtle, with the color only noticable on the turtleneck.
It really depends on the situation. As one example, the shiny metal insignia of a command officer in todays military is generally considered a bad idea to have on in the field because they screem "Sniper Target!". Instead they have colored but not shiny patches that you can see when you are face to face with the officer, but not at a long distance through a sniper scope. At least not as easily.
Have you're entire uniform be a different color depending on the department has the same problem, your command officers really stand out in the field.
Realistically, to me anyway, they could have one uniform for when they are on a ship and a different one when on a planet (in the field). In fact I believe the Navy, as an example, does just that.
Budget wise, that would have been expensive for the show, so I can understand why they never did that.